tbuckley/cabot-search huggingface dataset:
Cross Atlas Remapping via Optimal Transport (CAROT): Creating connectomes for different atlases when raw data is not available
Authors: Javid Dadashkarimi, Amin Karbasi, Qinghao Liang, Matthew Rosenblatt, Stephanie Noble, Maya Foster, Raimundo Rodriguez, Brendan Adkinson, Jean Ye, Huili Sun, Chris Camp, Michael Farruggia, Link Tejavibulya, Wei Dai, Rongtao Jiang, Angeliki Pollatou, Dustin Scheinost
Journal: Medical Image Analysis (2023)
Progress Toward Equitable Mpox Vaccination Coverage: A Shortfall Analysis — United States, May 2022–April 2023
Authors: Krishna Kiran Kota, Harrell Chesson, Jaeyoung Hong, Carla Zelaya, Ian H. Spicknall, Aspen P. Riser, Elizabeth Hurley, Dustin W. Currie, R. Ryan Lash, Neal Carnes, Jeniffer Concepción-Acevedo, Sascha Ellington, Ermias D. Belay, Jonathan Mermin
Journal: MMWR Morbidity and Mortality Weekly Report (2023)

More than 30,000 monkeypox (mpox) cases were reported in the United States during the 2022 multinational outbreak; cases disproportionately affected gay, bisexual, and other men who have sex with men (MSM). Substantial racial and ethnic disparities in incidence were also reported (1). The national mpox vaccination strategy* emphasizes that efforts to administer the JYNNEOS mpox vaccine should be focused among the populations at elevated risk for exposure to mpox (2). During May 2022-April 2023, a total of 748,329 first JYNNEOS vaccine doses (of the two recommended) were administered in the United States.† During the initial months of the outbreak, lower vaccination coverage rates among racial and ethnic minority groups were reported (1,3); however, after implementation of initiatives developed to expand access to mpox vaccination,§ coverage among racial and ethnic minority groups increased (1,4). A shortfall analysis was conducted to examine whether the increase in mpox vaccination coverage was equitable across all racial and ethnic groups (5). Shortfall was defined as the percentage of the vaccine-eligible population that did not receive the vaccine (i.e., 100% minus the percentage of the eligible population that did receive a first dose). Monthly mpox vaccination shortfalls were calculated and were stratified by race and ethnicity; monthly percent reductions in shortfall were also calculated compared with the preceding month's shortfall (6). The mpox vaccination shortfall decreased among all racial and ethnic groups during May 2022-April 2023; however, based on analysis of vaccine administration data with race and ethnicity reported, 66.0% of vaccine-eligible persons remained unvaccinated at the end of this period. The shortfall was largest among non-Hispanic Black or African American (Black) (77.9%) and non-Hispanic American Indian or Alaska Native (AI/AN) (74.5%) persons, followed by non-Hispanic White (White) (66.6%) and Hispanic or Latino (Hispanic) (63.0%) persons, and was lowest among non-Hispanic Asian (Asian) (38.5%) and non-Hispanic Native Hawaiian and other Pacific Islander (NH/OPI) (43.7%) persons. The largest percentage decreases in the shortfall were achieved during August (17.7%) and September (8.5%). However, during these months, smaller percentage decreases were achieved among Black persons (12.2% and 4.9%, respectively), highlighting the need for a focus on equity for the entirety of a public health response. Achieving equitable progress in JYNNEOS vaccination coverage will require substantial decreases in shortfalls among Black and AI/AN persons.
<i>Notes from the Field:</i> Chikungunya Outbreak — Paraguay, 2022–2023
Authors: Martha Torales, Amy Beeson, Lorena Grau, Miguel Galeano, Andrea Ojeda, Bettiana Martinez, Nancy León, Agueda Cabello, Fátima Rojas, Viviana de Egea, Rosa Galeano, Sandra Ocampos, Cynthia Vazquez, Romeo Montoya, Susan Hills, Guillermo Sequera
Journal: MMWR Morbidity and Mortality Weekly Report (2023)

Local transmission of chikungunya virus (CHIKV) was first reported in the Americas during December 2013, followed by widespread regional transmission (1).CHIKV is transmitted primarily by Aedes aegypti and Aedes albopictus mosquitoes.Most infected persons (72%-97%) experience symptomatic illness, typically including fever and often severe polyarthralgia (which can persist for months or years) (2).Rare complications include neurologic, cardiac, or renal disease (2).Paraguay reported its first autochthonous chikungunya case during 2015 (3).The subsequent outbreak, concentrated in the capital city of Asunción and the neighboring Central Department, resulted in 5,221 cases during 2015-2016.*A second outbreak (1,239 cases) occurred during 2018 in the north-central Amambay Department.Beginning the first week of October 2022, an increase in reported cases was again noted; this report provides preliminary information on this outbreak as of March 11, 2023.During October 1, 2022-March 11, 2023, a total of 81,037 suspected, probable, or confirmed † chikungunya cases was recorded by the Paraguayan Ministry of Health § ; among these, 75,911 (94%) occurred during 2023.Most cases occurred in Central Department (49,070; 61%) and Asunción (16,094; 20%).Cumulative national incidence was 1,073 cases per 100,000 population (3,088 per 100,000 population in Asunción).¶ Weekly case counts in Asunción and Central Department declined slightly after epidemiologic week 6, but an increasing number and proportion of cases were * https://www.mspbs.gov.py/dependencias/portal/adjunto/0a6e46-SE82023Alerta.
Surveillance To Track Progress Toward Poliomyelitis Eradication — Worldwide, 2021–2022
Authors: Tasha Stehling-Ariza, Amanda L. Wilkinson, Ousmane M. Diop, Jaume Jorba, Humayun Asghar, Tigran Avagnan, Varja Grabovac, Ticha Johnson, Sudhir Joshi, Anfumbom K. W. Kfutwah, Lucky Sangal, Salmaan Sharif, Ashraf Wahdan, Graham F. Tallis, Stephanie D. Kovacs
Journal: MMWR Morbidity and Mortality Weekly Report (2023)

Since the Global Polio Eradication Initiative (GPEI) was established in 1988, the number of wild poliovirus (WPV) cases has declined by >99.9%, and WPV serotypes 2 and 3 have been declared eradicated (1). By the end of 2022, WPV type 1 (WPV1) transmission remained endemic only in Afghanistan and Pakistan (2,3). However, during 2021-2022, Malawi and Mozambique reported nine WPV1 cases that were genetically linked to Pakistan (4,5), and circulating vaccine-derived poliovirus (cVDPV) outbreaks were detected in 42 countries (6). cVDPVs are oral poliovirus vaccine-derived viruses that can emerge after prolonged circulation in populations with low immunity allowing reversion to neurovirulence and can cause paralysis. Polioviruses are detected primarily through surveillance for acute flaccid paralysis (AFP), and poliovirus is confirmed through stool specimen testing. Environmental surveillance, the systematic sampling of sewage and testing for the presence of poliovirus, supplements AFP surveillance. Both surveillance systems were affected by the COVID-19 pandemic's effects on public health activities during 2020 (7,8) but improved in 2021 (9). This report updates previous reports (7,9) to describe surveillance performance during 2021-2022 in 34 priority countries.* In 2022, a total of 26 (76.5%) priority countries met the two key AFP surveillance performance indicator targets nationally compared with 24 (70.6%) countries in 2021; however, substantial gaps remain in subnational areas. Environmental surveillance expanded to 725 sites in priority countries, a 31.1% increase from the 553 sites reported in 2021. High-quality surveillance is critical to rapidly detect poliovirus transmission and enable prompt poliovirus outbreak response to stop circulation. Frequent monitoring of surveillance guides improvements to achieve progress toward polio eradication.
<i>Notes from the Field</i>: Rift Valley Fever Outbreak — Mbarara District, Western Uganda, January–March 2023
Authors: Zainah Kabami, Alex R. Ario, Richard Migisha, Helen Nelly Naiga, Annet Martha Nankya, Peter Ssebutinde, Christopher Nahabwe, Santos Omia, Francis Mugabi, David Muwanguzi, Allan Muruta, Joshua Kayiwa, Samuel Gidudu, Daniel Kadobera, Luke Nyakarahuka, Jimmy Baluku, Stephen Balinandi, Caitlin M. Cossaboom, Julie R. Harris
Journal: MMWR Morbidity and Mortality Weekly Report (2023)
Histamine-releasing factor in severe asthma and rhinovirus-associated asthma exacerbation
Authors: Yu Kawakami, Ikuo Takazawa, Merritt L. Fajt, Kazumi Kasakura, Joseph Lin, Julienne Ferrer, David B. Kantor, Wanda Phipatanakul, Peter W. Heymann, Chris A. Benedict, Yuko Kawakami, Toshiaki Kawakami
Journal: Journal of Allergy and Clinical Immunology (2023)
OnabotulinumtoxinA improves oral aperture in patients with scleroderma: A small clinical trial
Authors: Cristian D. Gonzalez, Jarod John Pamatmat, Kevin M. Burningham, Michelle Yang, Heather W. Goff
Journal: Journal of the American Academy of Dermatology (2023)

Reduced oral aperture (ROA), resulting from systemic sclerosis (SSc), is a debilitating condition with limited treatment options. Improvement in oral function has been reported with perioral administration of botulinum toxin type A.To prospectively evaluate the efficacy of onabotulinumtoxinA (onabotA) injection in improving oral opening and quality of life in SSc patients with ROA.Seventeen women with SSc and ROA were treated with 16 units of onabotA in 8 different sites around the cutaneous lips. Measurements of maximum mouth opening were taken before treatment, at 2 weeks posttreatment, and at 3 months posttreatment. Function and quality of life were also assessed via surveys.Interincisor and interlabial distances were significantly increased 2 weeks after treatment with onabotA (P < .001) but not 3 months after. Subjective improvement in quality of life was noted.This single-institution study enrolled 17 patients and did not have a placebo control group.OnabotA appears to have a strong short-term symptomatic benefit in patients with ROA due to SSc, with possible benefit to quality of life.
Noncoding RNA circuitry in melanoma onset, plasticity, and therapeutic response
Authors: Katerina Grafanaki, Ioannis Grammatikakis, Arin Ghosh, Vishaka Gopalan, Gulden Olgun, Huaitian Liu, George C. Kyriakopoulos, Ilias Skeparnias, Sophia Georgiou, Constantinos Stathopoulos, Sridhar Hannenhalli, Glenn Merlino, Kerrie L. Marie, Chi-Ping Day
Journal: Pharmacology & Therapeutics (2023)
Folic acid: The case to rethink the UK’s food fortification plans
Authors: Mun-Keat Looi
Journal: BMJ (2023)

The UK government has proposed adding folic acid to flour, to prevent hundreds of babies being born with neural tube defects each year. But is the recommended amount too low, asks <b>Mun-Keat Looi</b>, and should it be including other foodstuffs?
Combining rituximab with mycophenolate for the treatment of interstitial lung disease
Authors: Elizabeth R. Volkmann
Journal: European Respiratory Journal (2023)

Interstitial lung diseases (ILDs) encompass a heterogeneous group of diseases, including autoimmune ILD, hypersensitivity pneumonitis, occupational diseases, granulomatous diseases and idiopathic pneumonitis [1]. Despite their diverse aetiologies, ILDs share common clinical features and are a major contributor to disability and premature death [2]. In recent years, approved and emerging therapies for ILD have increased treatment options for patients [3]. This expanding therapeutic pipeline has created an opportunity to study how combining therapies may improve outcomes for patients with ILD. Combination therapy with rituximab and mycophenolate improves outcomes for patients with interstitial lung disease <https://bit.ly/3L5lKXU>
How does the MESA Lung Study sharpen blurry edges in interstitial lung abnormalities?
Authors: Pierre-Yves Brillet, Stéphane Tran Ba, Hilario Nunes
Journal: European Respiratory Journal (2023)

<b>McGroder and co-workers estimate the incidence of interstitial lung abnormalities (ILA) on non-contrast cardiac CT in the MESA study cohort and suggest that increased value of the percentage of high attenuation areas (%HAA) could precede occurrence of ILA</b>https://bit.ly/42yE96Q
Too hot? Too cold? Wnt signalling in pulmonary arterial hypertension: can we treat it “just right”?
Authors: Elena A. Goncharova, Tatiana V. Kudryashova, Soni Savai Pullamsetti
Journal: European Respiratory Journal (2023)

Pulmonary arterial hypertension (PAH) is a chronic, progressive and rapidly fatal disease with a poor prognosis, high mortality rate and lack of curative treatment options [1], defined by a mean pulmonary artery (PA) pressure greater than 20 mmHg at a rest [2, 3]. The main pathophysiological features of PAH include vasoconstriction, remodelling of small muscular PAs and perivascular inflammation [4]. PAH is a multifactorial disease. Genetic pre-disposition, epigenetic events, environmental exposure and other underlying conditions trigger endothelial cell (EC) apoptosis, leading to vascular pruning and loss of microvasculature, as well as cancer-like hyper-proliferation and survival of PA smooth muscle cells (PASMCs), PAECs and PA adventitial fibroblasts, and obstruction of small muscular PAs [1, 4, 5]. The functional and structural microvascular rarefaction results in the reduction in cross-sectional lumen area and in unresolved increase in right ventricular (RV) afterload, leading to premature death from right heart failure [6]. Dysbalanced Wnt signalling promotes pulmonary arterial hypertension <http://bit.ly/3ZvuNXf>
Blood-based biomarkers for Alzheimer’s disease: Current state and future use in a transformed global healthcare landscape
Authors: Harald Hampel, Yan Hu, Jeffrey Cummings, Soeren Mattke, Takeshi Iwatsubo, Akinori Nakamura, Bruno Vellas, Sid O’Bryant, Leslie M. Shaw, Min Cho, Richard Batrla, Andrea Vergallo, Kaj Blennow, Jeffrey Dage, Suzanne E. Schindler
Journal: Neuron (2023)
Advancing precision oncology in breast cancer: the FDA approval of elacestrant and guardant 360CDx: a correspondence
Authors: Haleema Qayyum Abbasi, Maryyum Adeena, Abdul Moiz Khan, None Syeda Shahnoor, Malik Olatunde Oduoye, Wechuli Polyne Nafula
Journal: International Journal of Surgery (2023)

Abbasi, Haleema Qayyum MBBSa; Adeena, Maryyum MBBSa; Khan, Abdul Moiz MBBSa; Syeda Shahnoor, MBBSb; Oduoye, Malik Olatunde MBBSc,d; Polyne Nafula, Wechuli MBBSe, Author Information
Endothelial cells in pulmonary fibrosis: more than a bystander
Authors: Toyoshi Yanagihara, Christophe Guignabert, Martin R.J. Kolb
Journal: European Respiratory Journal (2023)

<b>Focusing on EndMT, Wu et al. discovered that EC-like myofibroblasts are able to differentiate into myofibroblasts, resulting in a significant contribution to the pathogenesis of pulmonary fibrosis, and this process is redirected through induction of FoxA2</b> https://bit.ly/3YQvSIX
The GOLD 2023 proposed taxonomy: a new tool to determine COPD etiotypes
Authors: Joan B. Soriano, Andreas Horner, Michael Studnicka, Don D. Sin, Milo A. Puhan, Martijn A. Spruit, Bernd Lamprecht
Journal: European Respiratory Journal (2023)

The population burden of COPD remains high well into the 21st century, although with great regional variability [1]. Changes in the geographical and secular distribution of COPD points to the interaction of a number of risk factors beyond tobacco and other forms of smoking, which is still considered the first and foremost causal risk factor of COPD. We read with interest the new Global Initiative for Chronic Obstructive Lung Disease (GOLD) 2023 document, proposing a new taxonomy of COPD and suggesting six etiotypes on the origin of COPD [2]. This taxonomy is based on work found elsewhere [3, 4]. To the best of our knowledge, these etiotypes are not evidence-based, and the information required to obtain them has not been explored. We aimed to identify the information required to determine the classification of COPD etiotypes by GOLD 2023, by means of panel discussion and consensus by the authors. The information required to determine the classification of COPD etiotypes by GOLD 2023 is hard to obtain https://bit.ly/43ZJhCc All authors are members of the COPD Cohorts Collaborative International Assessment (3CIAplus) consortium, and aimed to determine COPD etiotypes in their pooled database.
Optimal implementation of the 2019 ESC/EAS dyslipidaemia guidelines in patients with and without atherosclerotic cardiovascular disease across Europe: a simulation based on the DA VINCI study
Authors: Julia Brandts, Sarah Bray, Guillermo Villa, Alberico L. Catapano, Neil R. Poulter, Antonio J. Vallejo-Vaz, Kausik K. Ray
Journal: The Lancet Regional Health - Europe (2023)

The impact of the stepwise implementation of the 2019 European Society of Cardiology (ESC)/European Atherosclerosis Society (EAS) treatment algorithm on low-density lipoprotein cholesterol (LDL-C) goal attainment was simulated in patients from the DA VINCI study.Monte Carlo simulation was used to evaluate treatment optimisation scenarios, based on a patient's risk category: statin intensification (step 1), addition of ezetimibe (step 2), and addition of a proprotein convertase subtilisin/kexin type 9 (PCSK9) inhibitor (step 3). Residual cardiovascular risk and predicted relative and absolute risk reduction (RRR and ARR) in cardiovascular events were assessed.In DA VINCI, 2482 patients did not achieve their 2019 ESC/EAS LDL-C goals and were included in the simulation. In patients without atherosclerotic cardiovascular disease (ASCVD) (n = 962), 27.0% (n = 259) and 57.0% (n = 548) are likely to achieve their LDL-C goals at step 1 and step 2, respectively. Of those at very high risk without ASCVD (n = 74), 88.1% (n = 65) are likely to achieve their LDL-C goals at step 3. In patients with ASCVD (n = 1520), 12.0% (n = 183), 42.1% (n = 641) and 93.2% (n = 1416) are likely to achieve their LDL-C goals at steps 1, 2 and 3, respectively. In patients with and without ASCVD, treatment optimisation may result in mean simulated RRR of 24.0% and 17.7%, respectively, and ARR of 8.1% and 2.6%, respectively.Most patients at high cardiovascular risk are unlikely to achieve LDL-C goals through statin optimisation and ezetimibe, and will require a PCSK9 inhibitor, leading to greater reduction in cardiovascular risk.Amgen.
Prognostic Role of Dynamic CZT Imaging in Heart Failure With Preserved Ejection Fraction
Authors: Kristina V. Kopeva, Andrey V. Mochula, Alina N. Maltseva, Mikhail V. Soldenko, Elena V. Grakova, Konstantin V. Zavadovsky
Journal: Clinical Nuclear Medicine (2023)

Objective The objective of the study was to evaluate the prognostic role of myocardial flow reserve (MFR) and myocardial blood flow (MBF) estimates obtained with dynamic cadmium-zinc-telluride (CZT) imaging in the development and progression of heart failure with preserved ejection fraction (HFpEF) in patients with nonobstructive coronary artery disease (CAD) during a 12-month follow-up period. Patients and Methods A total of 112 patients (70 men; median age of 62.5 [57.0; 69.0] years) with nonobstructive coronary artery disease were enrolled in the study. Dynamic CZT-SPECT, echocardiography, and coronary CT angiography studies were performed baseline. Results Distribution of patients was performed by adverse events: group 1 comprised patients with adverse outcomes (n = 25), and group 2 comprised those without it (n = 87). Based on receiver operating characteristic analysis, the levels of MFR ≤1.62 (area under the curve [AUС], 0.884; Р &lt; 0.001), stress-MBF ≤1.35 mL/min per gram (AUС, 0.750; Р &lt; 0.001), and NT-proBNP ≥760.5 pg/mL (AUС, 0.764; Р = 0.001) were identified as cutoff values to predict adverse outcomes. Univariate analysis revealed that type 2 diabetes mellitus ( P = 0.044), the levels of MFR ≤1.62 ( P = 0.014), stress-MBF ≤1.35 mL/min per gram ( P = 0.012), NT-proBNP ≥760.5 pg/mL ( P = 0.018), and diastolic dysfunction ( P = 0.009) were potential risk factors for the development and progression of HFpEF. Multivariate analysis demonstrated that the values of NT-proBNP ≥760.5 pg/mL (odds ratio, 1.87; 95% confidence interval, 1.17–3.62; P = 0.027) and MFR ≤1.62 (odds ratio, 2.801; 95% confidence interval, 1.19–6.55; P = 0.018) were independent predictors of adverse outcomes. Conclusions Our data suggest that reduced MFR ≤1.62 obtained with dynamic CZT imaging and overexpression of NT-proBNP ≥760.5 pg/mL can individuate patients at high risk of development and progression of HFpEF during a 12-month follow-up period, independently of baseline clinical parameters and imaging variables.
Restriction of C1-inhibitor activity in hereditary angioedema by dominant-negative effects of disease-associated SERPING1 gene variants
Authors: Laura Barrett Ryø, Didde Haslund, Anne Bruun Rovsing, Rasmus Pihl, Wariya Sanrattana, Steven de Maat, Yaseelan Palarasah, Coen Maas, Steffen Thiel, Jacob Giehm Mikkelsen
Journal: Journal of Allergy and Clinical Immunology (2023)

Patients with hereditary angioedema experience recurrent, sometimes life-threatening, attacks of edema. It is a rare genetic disorder characterized by genetic and clinical heterogenicity. Most cases are caused by genetic variants in the SERPING1 gene leading to plasma deficiency of the encoded protein C1 inhibitor (C1INH). More than 500 different hereditary angioedema-causing variants have been identified in the SERPING1 gene, but the disease mechanisms by which they result in pathologically low C1INH plasma levels remain largely unknown.The aim was to describe trans-inhibitory effects of full-length or near full-length C1INH encoded by 28 disease-associated SERPING1 variants.HeLa cells were transfected with expression constructs encoding the studied SERPING1 variants. Extensive and comparative studies of C1INH expression, secretion, functionality, and intracellular localization were carried out.Our findings characterized functional properties of a subset of SERPING1 variants allowing the examined variants to be subdivided into 5 different clusters, each containing variants sharing specific molecular characteristics. For all variants except 2, we found that coexpression of mutant and normal C1INH negatively affected the overall capacity to target proteases. Strikingly, for a subset of variants, intracellular formation of C1INH foci was detectable only in heterozygous configurations enabling simultaneous expression of normal and mutant C1INH.We provide a functional classification of SERPING1 gene variants suggesting that different SERPING1 variants drive the pathogenicity through different and in some cases overlapping molecular disease mechanisms. For a subset of gene variants, our data define some types of hereditary angioedema with C1INH deficiency as serpinopathies driven by dominant-negative disease mechanisms.